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      Ten millennia of hepatitis B virus evolution

      1 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 4 , 2 , 3 , 5 , 2 , 2 , 3 , 6 , 2 , 2 , 2 , 7 , 7 , 2 , 8 , 9 , 2 , 10 , 2 , 3 , 2 , 11 , 2 , 2 , 12 , 2 , 13 , 2 , 3 , 14 , 15 , 2 , 3 , 2 , 3 , 2 , 2 , 3 , 9 , 2 , 3 , 2 , 2 , 16 , 2 , 3 , 2 , 17 , 2 , 18 , 2 , 19 , 2 , 5 , 2 , 3 , 2 , 3 , 2 , 3 , 2 , 3 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 11 , 11 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 44 , 44 , 44 , 19 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 41 , 41 , 60 , 61 , 61 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 65 , 68 , 25 , 69 , 70 , 71 , 71 , 72 , 73 , 74 , 75 , 76 , 39 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 75 , 86 , 87 , 88 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 55 , 55 , 96 , 65 , 97 , 98 , 99 , 100 , 101 , 102 , 58 , 103 , 103 , 104 , 105 , 36 , 51 , 89 , 106 , 46 , 107 , 108 , 109 , 110 , 111 , 112 , 22 , 38 , 113 , 114 , 115 , 115 , 34 , 116 , 117 , 118 , 36 , 29 , 23 , 15 , 15 , 119 , 120 , 121 , 122 , 123 , 124 , 22 , 125 , 126 , 127 , 128 , 11 , 129 , 129 , 25 , 119 , 41 , 41 , 20 , 130 , 131 , 132 , 2 , 3 , 2 , 3 , 133 , 2 , 3 , 2 , 3 , 122 , 2 , 3 , 2 , 5 , 2 , 3 , 2 , 3 , 134 , 2 , 3 , 1 , 2 , 3 , 135
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          Fitting Linear Mixed-Effects Models Usinglme4

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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                October 08 2021
                October 08 2021
                : 374
                : 6564
                : 182-188
                Affiliations
                [1 ]Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.
                [2 ]Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.
                [3 ]Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
                [4 ]Max Planck Institute for Infection Biology, 10117 Berlin, Germany.
                [5 ]Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany.
                [6 ]ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
                [7 ]Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany.
                [8 ]Department of Genetics, Harvard Medical School, Boston, MA, USA.
                [9 ]Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
                [10 ]Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
                [11 ]Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.
                [12 ]Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland.
                [13 ]Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia.
                [14 ]Al-Farabi Kazakh National University, Almaty, Kazakhstan.
                [15 ]Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan.
                [16 ]Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
                [17 ]Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA.
                [18 ]Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.
                [19 ]Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
                [20 ]State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany.
                [21 ]Museo Archeologico Regionale “Antonino Salinas”, 90133 Palermo, Italy.
                [22 ]Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.
                [23 ]Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia.
                [24 ]Sterlitamak Museum of Local History, Sterlitamak, Russia.
                [25 ]Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.
                [26 ]Samara State University of Social Sciences and Education, Samara, Russia.
                [27 ]Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia.
                [28 ]Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia.
                [29 ]Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain.
                [30 ]Department of Prehistory and Archaeology, National Distance Education University (UNED), Madrid, Spain.
                [31 ]Private Technical Archaeologist, 50196 La Muela, Spain.
                [32 ]Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain.
                [33 ]Technical Archaeologist, Government of Aragón, Spain.
                [34 ]Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.
                [35 ]University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany.
                [36 ]Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK.
                [37 ]INRAP, ARAR UMR 5138, Maison de l’Orient et de la Méditerranée, Lyon, France.
                [38 ]State Historical Museum, Moscow, Russia.
                [39 ]Nasledie Cultural Heritage Unit, 355006 Stavropol, Russia.
                [40 ]Department of Anthropology, The National Museum, Prague, Czech Republic.
                [41 ]Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic.
                [42 ]The City of Prague Museum, Prague, Czech Republic.
                [43 ]Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK.
                [44 ]Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK.
                [45 ]Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland.
                [46 ]Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.
                [47 ]Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.
                [48 ]Universidad de Matanzas, Matanzas, Cuba.
                [49 ]Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
                [50 ]Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico.
                [51 ]Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK.
                [52 ]Université Côte d’Azur, CNRS, CEPAM UMR 7264, Nice, France.
                [53 ]Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France.
                [54 ]Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia.
                [55 ]Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia.
                [56 ]Department of Anthropology, University of South Florida, Tampa, FL, USA.
                [57 ]Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA.
                [58 ]Istituto di Ricerca Genetica e Biomedica–CNR, Monserrato, Italy.
                [59 ]Private contractor, Cagliari, Sardinia, Italy.
                [60 ]Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey.
                [61 ]Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.
                [62 ]Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain.
                [63 ]Bioarchaeology Service, Museum of Civilizations, Rome, Italy.
                [64 ]Dipartimento Asia Africa e Mediterraneo, Università di Napoli L’Orientale, Napoli, Italy.
                [65 ]Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.
                [66 ]Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.
                [67 ]Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK.
                [68 ]Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
                [69 ]Astrakhan State University, Astrakhan, Russia.
                [70 ]SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany.
                [71 ]Department of Anthropology, Yale University, New Haven, CT 06511, USA.
                [72 ]National Museum of Antiquities, 2301 EC Leiden, Netherlands.
                [73 ]Institute of History, Archaeology and Ethnography, Dushanbe, Tajikistan.
                [74 ]Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany.
                [75 ]Cronos S.C. Arqueología y Patrimonio, Burgos, Spain.
                [76 ]Regional Historical Museum Varna, Varna, BG-9000, Bulgaria.
                [77 ]Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia.
                [78 ]Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia.
                [79 ]Museo de Sitio Pucllana, s/n Miraflores, 18 Lima, Peru.
                [80 ]Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.
                [81 ]Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.
                [82 ]National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia.
                [83 ]University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.
                [84 ]Institute of Biology, University of Hildeshein, Germany.
                [85 ]Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany.
                [86 ]State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany.
                [87 ]ArchaeoZoology in Siberia and Central Asia–ZooSCAn, CNRS–IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia.
                [88 ]Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands.
                [89 ]Royal Belgian Institute of Natural Sciences, Brussels, Belgium.
                [90 ]Center for Archaeological Sciences, University of Leuven, Belgium.
                [91 ]Dienst Archeologie–Stad Mechelen, Belgium.
                [92 ]UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
                [93 ]UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
                [94 ]Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA.
                [95 ]Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland.
                [96 ]Applied Archaeology School of Science, Institute of Technology Sligo, Ireland.
                [97 ]School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia.
                [98 ]Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria.
                [99 ]Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey.
                [100 ]Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA.
                [101 ]Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.
                [102 ]Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain.
                [103 ]Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.
                [104 ]Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain.
                [105 ]Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA.
                [106 ]Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
                [107 ]Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.
                [108 ]DFG Center for Advanced Studies “Words, Bones, Genes, Tools,” University of Tübingen, Tübingen, Germany.
                [109 ]South Tyrol Provincial Heritage Service, South Tyrol, Italy.
                [110 ]Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.
                [111 ]Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.
                [112 ]Department of Geological Sciences, University of Cape Town, Cape Town, South Africa.
                [113 ]Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey.
                [114 ]The Cultural Heritage Foundation, 722 12 Västerås, Sweden.
                [115 ]National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria.
                [116 ]School of Natural Sciences, University of Central Lancashire, Preston, UK.
                [117 ]Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.
                [118 ]Department of Biology, University of Turku, 20500 Turku, Finland.
                [119 ]Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan.
                [120 ]Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.
                [121 ]State Historical and Cultural Museum-Reserve “Berel,” Katon-Karagay district, East Kazakhstan region, Kazakhstan.
                [122 ]Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany.
                [123 ]Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.
                [124 ]Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany.
                [125 ]Department of Cultures, University of Helsinki, 00014 Helsinki, Finland.
                [126 ]Research Centre for Medical Genetics, Moscow, Russia.
                [127 ]Biobank of North Eurasia, Moscow, Russia.
                [128 ]Vavilov Institute of General Genetics, Moscow, Russia.
                [129 ]Eurasia Department, German Archaeological Institute, Berlin, Germany.
                [130 ]Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.
                [131 ]Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.
                [132 ]Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland.
                [133 ]Department of Anthropology, Harvard University, Cambridge, MA 02138, USA.
                [134 ]School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
                [135 ]European Virus Bioinformatics Center (EVBC), Jena, Germany.
                Article
                10.1126/science.abi5658
                34618562
                ecee9d52-ff98-4c78-89cb-ae465698ab63
                © 2021
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